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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A PAS DOMAIN FROM A SENSORY BOX HISTIDINE KINASE REGULATOR FROM GEOBACTER SULFURREDUCENS TO 2.5A
 
Authors :  A. J. Stein, A. Weger, E. Duggan, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  18 Feb 10  (Deposition) - 16 Mar 10  (Release) - 16 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Pas, Histidine, Kinase, Geobacter, Sulfurreducens, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Atp-Binding, Nucleotide-Binding, Phosphoprotein, Transferase, Two- Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Stein, A. Weger, E. Duggan, S. Clancy, A. Joachimiak
The Crystal Structure Of A Pas Domain From A Sensory Box Histidine Kinase Regulator From Geobacter Sulfurreducens To 2. 5A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SENSOR PROTEIN
    ChainsA, B, C, D
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneGSU1414
    Organism ScientificGEOBACTER SULFURREDUCENS
    Organism Taxid243231
    StrainPCA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)ABC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PGE5Ligand/IonTRIETHYLENE GLYCOL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PGE5Ligand/IonTRIETHYLENE GLYCOL
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 17)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2PGE5Ligand/IonTRIETHYLENE GLYCOL
3SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:159 , ARG B:180BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREARG A:180 , HOH B:6 , ARG B:159 , ARG B:176 , PHE B:195BINDING SITE FOR RESIDUE SO4 B 2
3AC3SOFTWAREALA A:98 , PRO A:99 , ALA A:100 , LEU A:102 , ARG B:90BINDING SITE FOR RESIDUE SO4 A 3
4AC4SOFTWAREPHE C:94 , PRO C:181BINDING SITE FOR RESIDUE PGE C 1
5AC5SOFTWAREARG A:90 , ALA B:100 , GLU B:178 , ARG B:180 , PHE B:195BINDING SITE FOR RESIDUE PGE B 201
6AC6SOFTWAREGLY C:170BINDING SITE FOR RESIDUE PGE A 201
7AC7SOFTWAREHIS C:134 , ILE C:141 , TRP C:145 , HIS C:149BINDING SITE FOR RESIDUE PGE C 4
8AC8SOFTWAREHIS B:134 , ILE B:141 , TRP B:145 , HIS B:149BINDING SITE FOR RESIDUE PGE B 5

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:164 -C:164
2B:164 -D:164

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu B:186 -Gly B:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LUQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LUQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3LUQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:112
 aligned with Q74DA3_GEOSL | Q74DA3 from UniProtKB/TrEMBL  Length:844

    Alignment length:114
                                    96       106       116       126       136       146       156       166       176       186       196    
         Q74DA3_GEOSL    87 SDERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh...eeeeee....eeeehhhhhhhh..........hhhhhh...hhhhhhhhhhhhh...eeeeeeeee.--..eeeeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3luq A  87 SDERLRLFTEHAPAALAmFDREmRYLAVSRRWREDYGLGDGDILGmSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVR--GRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 200
                                    96       106  |    116       126     | 136       146       156       166|  |   176       186       196    
                                           104-MSE|                    132-MSE                            167  |                              
                                                109-MSE                                                      170                              

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q74DA3_GEOSL | Q74DA3 from UniProtKB/TrEMBL  Length:844

    Alignment length:114
                                    96       106       116       126       136       146       156       166       176       186       196    
         Q74DA3_GEOSL    87 SDERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeeee.....eeeehhhhhhhhh.........hhhhhh...hhhhhhhhhhhhh...eeeeeeee.......eeeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3luq B  87 SDERLRLFTEHAPAALAmFDREmRYLAVSRRWREDYGLGDGDILGmSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 200
                                    96       106  |    116       126     | 136       146       156       166       176       186       196    
                                           104-MSE|                    132-MSE                                                                
                                                109-MSE                                                                                       

Chain C from PDB  Type:PROTEIN  Length:114
 aligned with Q74DA3_GEOSL | Q74DA3 from UniProtKB/TrEMBL  Length:844

    Alignment length:114
                                    96       106       116       126       136       146       156       166       176       186       196    
         Q74DA3_GEOSL    87 SDERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeeeee....eeeehhhhhhhh..........hhhhhh...hhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3luq C  87 SDERLRLFTEHAPAALAmFDREmRYLAVSRRWREDYGLGDGDILGmSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 200
                                    96       106  |    116       126     | 136       146       156       166       176       186       196    
                                           104-MSE|                    132-MSE                                                                
                                                109-MSE                                                                                       

Chain D from PDB  Type:PROTEIN  Length:110
 aligned with Q74DA3_GEOSL | Q74DA3 from UniProtKB/TrEMBL  Length:844

    Alignment length:112
                                    97       107       117       127       137       147       157       167       177       187       197  
         Q74DA3_GEOSL    88 DERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDI 199
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------PAS_4-3luqD01 D:95-199                                                                                    Pfam domains (1)
           Pfam domains (2) -------PAS_4-3luqD02 D:95-199                                                                                    Pfam domains (2)
           Pfam domains (3) -------PAS_4-3luqD03 D:95-199                                                                                    Pfam domains (3)
           Pfam domains (4) -------PAS_4-3luqD04 D:95-199                                                                                    Pfam domains (4)
         Sec.struct. author hhhhhhhhhh....eeeee....eeeehhhhhhhh..........hhhhhh...hhhhhhhhhhhhh...eeeeeeeee.....eeeeeeeeeeee.--..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3luq D  88 DERLRLFTEHAPAALAmFDREmRYLAVSRRWREDYGLGDGDILGmSHYDIFPEIGEEWKSVHRRGLAGEVIRVEEDCFVRADGRTQWLRWEVRPWYE--GRVGGVVIFTEDI 199
                                    97      |107 |     117       127    |  137       147       157       167       177      |187       197  
                                          104-MSE|                    132-MSE                                             184  |            
                                               109-MSE                                                                       187            

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3LUQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LUQ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q74DA3_GEOSL | Q74DA3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    GO:0004673    protein histidine kinase activity    Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0018106    peptidyl-histidine phosphorylation    The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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